ImmunoGraph MCP

generate_candidate_peptides

Read-onlyIdempotent

Enumerate one-based peptide windows from a protein sequence for MHC-I or MHC-II exploration, returning peptide, start, end, and length for downstream binding prediction.

Instructions

Enumerate one-based peptide windows from a supplied protein sequence for MHC-I or MHC-II exploration. Use after validate_sequence and before prediction; this creates candidates, not binding scores. Returns each window with peptide, start, end, and length.

Input Schema

Name	Required	Description	Default
`runId`	No	Caller-chosen identifier linking this call to one research run.	interactive-run
`sequence`	Yes	Protein amino-acid sequence without a FASTA header.
`sequenceHash`	No	Optional SHA-256 identity of the supplied protein sequence.
`candidateType`	Yes	MHC class or candidate category this operation applies to.
`peptideLengths`	Yes	Peptide window lengths in amino-acid residues for the selected MHC class.

Output Schema

Name	Required	Description
`ok`	Yes	Whether execution completed successfully.
`data`	No	Tool-specific result fields on success.
`meta`	Yes	Run identifiers, timings, and input/output hashes.
`error`	No	Structured failure on unsuccessful execution.

Schema Changelog

Changes observed during successful MCP inspections.

Changed6 schema fields changedv0.2.1Oct 31, 2026

addedInput schema / properties / candidateType / description

Added value: +"MHC class or candidate category this operation applies to."

addedInput schema / properties / peptideLengths / description

Added value: +"Peptide window lengths in amino-acid residues for the selected MHC class."

addedInput schema / properties / runId / description

Added value: +"Caller-chosen identifier linking this call to one research run."

addedInput schema / properties / sequence / description

Added value: +"Protein amino-acid sequence without a FASTA header."

addedInput schema / properties / sequenceHash / description

Added value: +"Optional SHA-256 identity of the supplied protein sequence."

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "additionalProperties": {},
+  "properties": {
+    "data": {
+      "additionalProperties": {},
+      "description": "Tool-specific result fields on success.",
+      "properties": {},
+      "type": "object"
+    },
+    "error": {
+      "additionalProperties": false,
+      "description": "Structured failure on unsuccessful execution.",
+      "properties": {
+        "category": {
+          "type": "string"
+        },
+        "code": {
+          "type": "string"
+        },
+        "details": {
+          "additionalProperties": {},
+          "properties": {},
+          "type": "object"
+        },
+        "message": {
+          "type": "string"
+        },
+        "retryable": {
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "code",
+        "category",
+        "message",
+        "retryable"
+      ],
+      "type": "object"
+    },
+    "meta": {
+      "additionalProperties": {},
+      "description": "Run identifiers, timings, and input/output hashes.",
+      "properties": {
+        "completedAt": {
+          "type": "string"
+        },
+        "durationMs": {
+          "type": "number"
+        },
+        "inputHash": {
+          "type": "string"
+        },
+        "outputHash": {
+          "type": "string"
+        },
+        "requestId": {
+          "type": "string"
+        },
+        "runId": {
+          "type": "string"
+        },
+        "startedAt": {
+          "type": "string"
+        },
+        "toolName": {
+          "type": "string"
+        },
+        "toolVersion": {
+          "type": "string"
+        }
+      },
+      "required": [
+        "requestId",
+        "runId",
+        "toolName",
+        "toolVersion",
+        "startedAt",
+        "inputHash"
+      ],
+      "type": "object"
+    },
+    "ok": {
+      "description": "Whether execution completed successfully.",
+      "type": "boolean"
+    }
+  },
+  "required": [
+    "ok",
+    "meta"
+  ],
+  "type": "object"
+}

First observedv0.2.0Oct 31, 2026

TDQS

A4.6/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint and idempotentHint, and the description is consistent with them (pure enumeration, no scoring). It adds useful behavioral context by clarifying that the output is candidate windows rather than ranked results, but it does not mention edge behavior such as sequences shorter than the requested peptide lengths or invalid residues.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three short sentences, front-loaded with what the tool does, then when to use it, then what it returns. No filler and nothing repeated from the schema.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a 5-parameter enumeration tool with an output schema, the description covers purpose, ordering, and non-scoring semantics adequately. Minor gaps remain around failure modes (too-short sequence, invalid amino acids) and how many windows are produced, but the output schema carries the return-value burden.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline is 3, but the description adds genuine semantics beyond the schema: 'one-based' indexing (which the start/end parameters never state) and the peptide/start/end/length shape produced per window. It still doesn't clarify how candidateType interacts with peptideLengths choices.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ('Enumerate one-based peptide windows from a supplied protein sequence') with the MHC-I/MHC-II scope. It also explicitly contrasts with the prediction siblings by saying 'this creates candidates, not binding scores', so an agent can distinguish it from predict_mhci/predict_mhcii without opening a schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives explicit pipeline positioning ('Use after validate_sequence and before prediction'), naming the sibling that precedes it and the class of siblings that follows. It also names the exclusion — this does not produce binding scores — so the boundary against prediction tools is stated, not inferred.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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